Genetics And Cell Biology Flashcards
Describe features of prokaryotes and eukaryotes
Prokaryotes:
- 2 groups or domains: archaea and bacteria
- no organelles
- no nucleus
- DNA with circular genome
- most diverse kind of cells
Eukaryotes:
- have discrete organelles
- have a nucleus (membrane bound structure containing DNA)
- have mitochondria
- have others such as Golgi and endoplasmic reticulum and lysosomes etc
- different types of cells for different functions
Draw a labelled diagram of a cell membrane
See lecture 1
Label a diagram of a mammalian cell
See lecture 1
Define cellular homeostasis
the property of a system, especially a living organism, to regulate its internal environment so as to maintain a stable, constant condition
Why do cells maintain homeostasis
Key things (like temperature, pH, osmolality, ionic concentrations etc) have to be kept in narrow tolerances
How is homeostasis maintained
- alter properties
- programmed cell death (apoptosis) necessary in multicellular animals
- infected or unhealthy cells “commit suicide” (altruism)
How many bonds are between adenine and thymine
2
How many bonds are between cytosine and guanine
3
Describe how covalent bonds and ionic bonds allow for stable arrangement of atoms
Both form strong bonds
Covalent bonds: between 2 non-metals and similar electronegativity
Ionic bonds: between metal and non- metals with different electronegativity
What are homopolymers
Polymers that are made of many copies of the same molecule
What are heteropolymers
Polymers created from different assemblies of different building blocks
What are the four main polymers found in cells? Give a brief description of each
- Polysaccharides: polymers of sugars - typically homopolymers
- Fats/lipids: polymers of carbons with other groups attached
- Nucleic acids: polymers of nucleotide bases in specific sequences ( heteropolymers)
- Proteins: polymers of 20 different amino acids in specific sequences (heteropolymers)
Describe the key components of sugars
- simplest are monosaccharides- (CH2O)n
- can be drawn as chains or rings - alpha and beta links (hydroxyl group on the carbon that carries aldehyde or ketone can rapidly change from one position to the other)
- disaccharides are simple polysaccharides (formed by glycosidic bonds)
- large linear and branched molecules can be made from simple repeating units - short chains are called oligosaccharides and long chains are called polysaccharides eg cellulose and glycogen
- glycogen is the stable storage form of glucose in the body
- cell surface glycoproteins are proteins with sugar on top
- one sugar group determines the difference between the ABO blood groups
How do you form sucrose, maltose and lactose
Sucrose = glucose + fructose Maltose = glucose + glucose Lactose = glucose + galactose
Describe the key properties of fatty acids
- components of cell membranes
- stored in the cytoplasm as triacylglcerol - can be released from it when a cell needs energy (done via acetyl CoA)
- saturated fats have no double bonds (solids and not very reactive)
- unsaturated fats have double bonds (don’t pack well and are quite reactive + they are oils)
- phospholipids aggregate to form cell membranes
- proteins are embedded in the plasma membrane lipid bilayer (can have many key roles eg transporters, anchors, receptors, enzymes)
What does amphipathic mean
Both hydrophilic and hydrophobic regions
Describe the key properties of nucleic acids
- form nucleotides
- basis of DNA and chromosomes
- nucleotides perform a variety of functions in cells
1. Carry chemical energy in their easily hydrolysed phosphoanhydride bonds
2. Combine with other groups to form coenzymes
3. Used as signalling molecules in the cell
Draw the general formula for an amino acid
See lecture 2 slide 36
Give two examples of diseases caused by protein assembly going wrong. Briefly describe each
- Cystic fibrosis: mutations in Cl- ion channel cause a misfolding of the channel that prevents correct Cl- transport
- Alzheimer’s disease: misfolding and aggregation of a protein called b-amyloid
Sketch a labelled diagram of a double stranded DNA molecule. To which end are new bases added
See lecture 3 slide 7
What is the sugar in RNA and what is it in DNA
RNA = ribose DNA = deoxyribose
What group the bases in DNA and RNA into purines and pyrimidines
Purines: Adenine and Guanine
Pyrimidines: cytosine, thymine and uracil
Draw a simple labelled diagram of DNA replication at the replication fork
See lecture 3 slide 13
What is released when a base is added during DNA synthesis
Pyrophosphate
P2O7^4-
What enzyme catalyses DNA replication. Describe in one sentence what it does
DNA polymerase
It catalyses the addition of nucleotides to the growing end (3’ OH) of a new DNA molecule, it stays attached to the DNA and adds new bases stepwise
How is DNA made in the “lagging strand” where the direction is 5’ to 3’
- short strands called Okazaki fragments are made in the 5’ to 3’ direction
- these strands are made in small pieces discontinuously
- DNA ligand joins them together via “backstitching”
What is the main enzyme involved in transcription
RNA polymerase
Describe alternative splicing
Some RNAs use different combinations of exons to form different proteins
Different tissues can express different versions of the same RNA generated by alternative splicing
What are the start and end codons
Start - Met (AUG)
End - UGA, UAA, UAG
Give two examples of congenital diseases caused by genetics
Down’s syndrome
Cystic fibrosis
What is the definition of a diagnosis of a genetic disease
Testing of patient, following indicative clinical findings, to confirm genetic diagnosis
Definition of newborn screening
Testing of newborn to identify conditions that require immediate initiation of treatment to prevent death or disability
Definition of carrier tests
Testing to identify an asymptomatic adult who is a carrier for autosomal-recessive or X-linked recessive conditions. Testing is usually initiated in the basis of family history or because the genetic condition is common among individuals of the patients ethnicity
Definition of prenatal tests
Testing to identify a foetus with a genetic condition. Testing is usually initiated on the basis of maternal factors or family history that indicate increased risk
Definition for tests for adult-onset genetic conditions
Testing of asymptomatic young adults to identify a genetic condition that will occur later in life, such as Huntington’s disease
Why is it particularly important that diagnostic and susceptibility tests have no (very low) false negative rate and a low false positive rate
No false negative rate: tell ppl they don’t have it - but they actually do - means you can end up missing ppl
Low false positive rate: identify that they have it but they don’t actually - must always follow up to confirm
Name 3 things along with examples of each that can be tested for in a diagnostic or susceptibility test
Chromosomes - trisomy 21; Down syndrome
Specific mutations - cystic fibrosis
Specific gene - polycystic kidney disease
Give 5 examples of things NIPT is good to detect
Down syndrome Edwards syndrome Palau syndrome Turner syndrome Fetal sex determination
What population (prenatal) screening occurs in the UK
Downs and Edwards and Pataus syndrome combined test
Sickle cell disease
Thalassaemia
Newborn and infant physical examination (NIPE) screens newborns within 72 hours of birth
General foetal screening by careful ultrasound examination for structural abnormalities
Give an example of a disease identified through newborn screening
Sickle cell disease
Cystic fibrosis
Congenital hypothyroidism
How is transcription regulated
DNA packaged around histone proteins: Chromatin Histone modification (acetylation) regulates access to the DNA Histone acetylation increases transcription
What do transcription factors do
Create conditions for transcription
What do microRNA do and how do they do it
miRNAs regulate mRNAs
Work as part of RISC (RNA-Induced Silencing Complex)
miRNAs ‘tell’ RISC which mRNAs to target
miRNAs bind to mRNA - specific RNA sequence - complimentary
They do it by:
Causing them to be degraded
Prevent them from being translated
Give two clinical examples of how circulating microRNAs can be used as biomarkers
Clinical applications to date
Cardiovascular disease
Cancer
- Clinical test to differentiate between chronic pancreatitis and pancreatic cancer (Asuragen)
- Cancer Origin Test™ (Rosetta)
How can PCR be used in diagnostics
Virology (multiply virus to check if it’s there)
Detection of bacteria
Forensics and paternity kits
All genetic tests
4 applications of NGS
Mutation detection
Pharmacogenetics
Gene expression
Microbiology
Draw and label a diagram of a chromosome
See lecture 5
Slide 12
What is a nucleosome
DNA wrapped around 8 his tone proteins
What is chromatin
Network of DNA & proteins that make up chromosomes during interphase
What is heterochromatin
Highly condensed and genetically inactive
What is euchromatin
Lighter staining, relatively open structure where genes may be accessed and are active
Draw the four classifications of chromosomes
See lecture 5
Slide 15
Describe mitosis
See lecture 5
Slide 18
Describe meiosis
See lecture 5
Slide 19
what does ploidy and aneuploidy mean
Ploidy: wrong number of complete chr sets
Aneuploidy: specific additional or missing chromosomes
Which bases are the purines and which bases are the pyrimidines
Purines are adenine and guanine
Pyrimidines are cytosine and thymine
list the different types of DNA mutation
Point mutations Insertions and deletions Gene deletions Translocations Complex chromosomal rearrangements
what are transitions and transversions in relation to DNA bases
Transitions are interchanges of two-ring purines (A G) or of one-ring pyrimidines (C T): they therefore involve bases of similar shape.
Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures
What are the three types of point mutation? Describe them
Silent - no change in protein
Nonsense - incomplete protein - mutation causes a stop codon
Missense - faulty protein - codon changes which protein is made
How can the location of a mutation change its effect
In the coding sequence
- change the protein or stop translation
In the promoter or non-coding regions
- Alter expression levels
Describe triplet repeat disorders and list 3 disease examples
Triplet repeat disorder occur due to an increase in the number of specific triplet repeats. Conditions tend to get worse through generations (anticipation) as the number of repeats increases due to errors during replication. The effects depend upon the location of the repeat, whether in coding regions (eg polyQ conditions) or in non-coding regions.
Examples include Fragile X Syndrome, Myotonic Dystrophy, Huntington Disease
What type of mutation causes Cystic fibrosis and what kind of inheritance is it
Deletion of the codon for the 508th amino acid (phenylalanine, F) in the cystic fibrosis conductance regulator (CFTR) gene
Autosomal recessive
What type of mutation causes sickle cell disease and what kind of inheritance is it
Single nucleotide missense mutation
Autosomal recessive
What kind of mutation causes Beta Thalassemia and describe its inheritance pattern
Lots of mutations - mostly point mutations
Severity depends on mutation
Heterozygous state - mild
Homozygous state - moderate or severe
What type of mutations cause haemophilia and what is it’s pattern of inheritance
X linked recessive
Simple and complicated mutations:
Deletions, point and rearrangements
Compare the influence of different gene mutations upon the pattern of inheritance of a disease
Gain of function often dominant inheritance, eg Huntingdon’s disease
Loss of function usually recessive, eg thalassaemia
Loss of function of gene on X chromosome X-linked recessive, eg haemophilia
Fragile X mental retardation causes loss of function but this has a dominant effect (ie males with one mutated copy are affected) – this is X-linked dominant inheritance.
Give 4 treatment strategies for genetic diseases. Give examples for each
- Gene therapy, e.g. vector-based (eg adenovirus),CRISPR-Cas9, CAR T (Acute Lymphoblastic Leukaemia & Diffuse Large B-Cell Lymphoma)
- Block downstream cellular pathway (eg Sirolimus in Tuberous Sclerosis)
- Enzyme replacement, e.g. Alpha-Galactosidase in Fabry Disease
- Substrate reduction, eg some enzyme deficiencies
What does aneuploidy mean
Abnormal number of chromosomes within a cell
What does mosaicism mean
Different populations of cells with different numbers of chromosomes
How does FISH work
Uses specific dye-labelled DNA sequence to hybridise to chromosomal region of interest
A patient shows these symptoms, what is the syndrome? Cardiac abnormalities Thymic hypoplasia; T cell abnormalities Hypocalcaemia Cleft palate Abnormal ears, micrognathia Broad nose Long slender fingers Developmental delay Autistic spectrum disorder
DiGeorge syndrome
A patient shows these symptoms, what is the syndrome?
Saggy cheeks, widespaced teeth, full lips, stellate irides
Joint laxity
Developmental delay
“Cocktail party” speech & personality
Supravalvular aortic stenosis
Hypercalcaemia
Deletion knocks out Elastin gene on chr 7
Williams Syndrome
Describe Amniocentesis
Usually between 14-18 weeks ofpregnancy
Risk of miscarriage
Can analyse amnioticfluid, & cells
Describe Chorion Villus Sampling (CVS)
Samples contain cellular fetal material
Suitable for direct enzyme analysis & DNA extraction
CPM (confined placental mosaicism)
Good for T1 diagnosis of single gene & metabolic disorders
Describe Non-invasive prenatal testing (NIPT)
Cell-free fetal DNA in maternal circulation (>6wks)
Y chromosomal material
- PRESENT: male fetus
- ABSENT: female fetus
Quantification of specific chromosomal sequences, eg Tri 21
Indentification of paternal mutations, eg HD
BRCA1 & BRCA2 breast/ovarian cancer:
What is the pattern of inheritance?
What kind of screening can be done?
What kind of surgery can be done to reduce risk?
Males and females can carry the gene
MRI, mammogram, ovarian screening
Mastectomy & bilateral saplingo-oophorectomy
What are the main symptoms of Retinitis Pigmentosa
Primarily affects rod photoreceptors:
- night blindness, loss of peripheral vision, ultimately loss of central vision
Extremely heterogeneous
Describe the genetic heterogeneity in Cystic Fibrosis and how this influences patient outcome/treatment
One diseases - one gene - many mutations
Mutations in CFTR gene which encodes an ion channel - normal channel moves chloride ions fo outside of cell whereas mutant CFTR channel does not
Can be too few and/or dysfunctional channels
Genetic diagnosis can guide therapy:
- identify class of defect
Therefore can be treated with:
- correctors - increase quantity of protein produced
- potentiators - enhance remaining CFTR function
Outline the extensive genetic heterogeneity underlying Retinitis Pigmentosa
One disease - many genes - many mutations
What are DNA markers
Regions of DNA that vary between individuals
Chromosomal location known
Allows you to see if the disease gene is close to or ‘linked’ to the DNA marker
Repeated sequences
<6 bp: Microsatellites /Short tandem repeats (STRs)
Minisatellites/Variable number tandem repeats (VNTRs)
Single nucleotide polymorphisms (SNPs)
What is genetic heterogeneity
Genetic heterogeneity is a phenomenon in which a single phenotype or genetic disorder may be caused by any one of a multiple number of alleles from the same gene or mutations in several genes.
What is Pleiotropy
Single gene contributes to multiple phenotypic traits
What is the difference between Mendelian and multifactorial disease
Mendelian - one mutation on one gene
Multifactorial - involve other genes or factors such as environment
Describe what is meant by fully penetrant conditions
Other genes and environmental factors have no apparent effect
What is meant by low-penetrance genes
They have a small influence, along with other genetic and environmental factors
What does llambda symbol represent in family studies and what does the subscript denote
Risk ratio
Subscript letter denotes the family relationship/member for whom the ratio was calculated
In twin studies what do these terms mean
a) monozygotic
b) dizygotic
c) concordant
d) discordant
a) identical twins
b) non-identical twins
c) both twins are affected or unaffected
d) only one twin is affected
Define the differences between inherited and somatic cancer
Inherited then it must show that it has been passed on through the family - certain forms are inherited but not all
Define the key hallmarks of cancer
- self-sufficiency in growth signals
- insensitivity to antigrowth signals
- tissue invasion and metastasis
- limitless replicative potential
- sustained angiogenesis
- evading apoptosis
Outline the most relevant molecular mechanisms in the development of cancer
- translocation or transposition - gene moved to new locus, under new controls - give rise to producing a lot of copies of a particular gene
- gene amplification - multiple copies of the gene
- point mutation within a control element
- point mutation within the gene - hyperactive or degradation-resistant protein
List example roles of genetics in human congenital abnormalities
Down’s syndrome - chromosome abnormalities
Cystic fibrosis - single gene disorder
Describe key differences and similarities between diagnostic, presymptomatic, carrier, and susceptibility genetic testing
Diagnostic:
Testing patient, following clinical findings to confirm genetic diagnosis
Presymptomatic:
- Newborn screening: test newborn to identify immediate conditions that require immediate initiation of treatment to prevent death or disability
- Prenatal testing: identify fetes with a genetic condition. Usually initiated on the basis of maternal factors or family history that indicate increased risk. However sometimes offered routinely
Carrier:
To identify an asymptomatic adult who is a carrier for autosomal-recessive or X-linked recessive conditions. Usually initiated on basis of family history
Genetic:
- Tests for adult onset genetic conditions: asymptomatic young adults to identify condition that will occur later in life
Susceptibility;
- Assessment of genetic risk for common complex diseases - identify an increased risk of future health problems eg heart disease or diabetes
Compare options for population-based screening of ‘single gene’ and complex diseases
Single Gene:
- Chromosomes: cytogenetic analysis - Down Syndrome
- Specific mutation: testing known mutation in the family - cystic fibrosis
- Specific gene
Complex Diseases:
- Panel of genes: test multiple genes that might harbour the disease causing gene
- Whole Genome: NGS of all 3 billion bases in human genome
Define why population ancestry may be important
The frequency of genetic variation varies between populations of different ancestry
Describe examples of current population genetic screening programmes and recognise basic parameters governing population genetic screening
- Down’s, Edwards’ & Patau’s syndrome combined test
- Sickle cell disease
- Thalassaemia
- Newborn and infant physical examination (NIPE)
- tests for congenital heart disease
developmental dysplasia of the hip
congenital cataracts
cryptorchidism (undescended testes) - Ultrasound
- Newborn blood spot test
Considerations:
- inform diagnosis/prognosis?
- inform treatment?
- is there support available?
- reliable?
- consent?
- when do you tell them unexpected findings?
How do transcription factors regulate gene expression
Molecular switches
DNA packaged in chromosome
Activator binds regulatory elements
Transcription factors and RNA polymerase recruited
Transcription activated
How do microRNAs effect gene expression
Regulate the expression of many mRNAs by binding to sequences in the 3’ untranslated region of protein coding genes
What is genetic imprinting
Determination of gene expression by parental origin
How does DNA methylation work
Gene inactivation
Methylation (addition of CH3) occurs on cytosine of CpG’s (when cytosine lies next to guanine in the DNA sequence)
Forms 5-methyl cytosine
Is reversible
Can be inherited or changed with drugs/lifestyle
Draw the main pedigree symbols for:
Male, female, sex undesignated, adopted, pregnancy, deceased, affected with trait, carrier for trait, carrier for x linked trait, mating, consanguineous mating, siblings, divorced or separated, miscarriage, dizygotic twins, monozygotic twins, no offspring, patient initiating genetic work up, two matings
See tutorial two
What are the three main functions of the plasma membrane
- Receiving information
- Import and export of molecules
- Capacity for movement and expansion
What does amphipathic mean in relation to the plasma membrane
Contains both hydrophilic and hydrophobic bits
What will pure phospholipids form in water
Liposomes
Which will dissolve in water - hydrophyllic or hydrophobic molecules
Hydrophyllic
What does the fluidity of the plasma membrane depend on
- Which phospholipids are present
- The properties of hydrocarbon tails:
- length: short chains - increases fluidity (18-20 carbon atoms is typical length)
- number of double bonds - double bonds increase fluidity - decreasing packaging
How does surfactant in lungs keep airways open
Alveoli in lungs requires surfactant
It decreases surface tension and allows bubbles to form in alveoli which keeps airways open
What effect does cholesterol have on the plasma membrane
Stiffens up cell membranes
Prevents fluidity
Fills spaces between phospholipids left by their kinks from the unsaturated hydrocarbon tails - this decreases fluidity
Why is membrane fluidity important
- Allows membrane proteins to diffuse in the 2D-plane of the membrane
- allows membrane lipids to move within the bilayer
- allows membranes to fuse with each other and exchange contents
- ensures equal distribution of cell contents between daughter cells when a cell divides
What phospholipid is always on the inside layer of the plasma membrane
Phosphatidylinositol (PI)
What do flip-flop enzymes do. Explain the 3 types
Move lipids across the bilayer
Flippases: outside in
Floppases: inside out
Scramblases: both directions
What are glycoproteins and what is their function
Sugars attached to proteins
Protect cell from damage
Slimy surface
Involved in cell-cell communication
Give cells particular identity (eg can tell if liver cell, fat cell etc)
What is the cell cortex
Mesh like structure
Protein framework
Supports and strengthens cell membrane
Briefly describe passive and active transport
Passive: passage along concentration gradient - no energy needed
Active: against concentration gradient - requires energy - involves 2 types of membrane proteins: transporters and ion channels
Name examples of local and long distance cell signalling
Local:
- contact
- paracrine
- aurocrine
- synaptic
Long distance:
- endocrine
- neuronal
Describe paracrine signalling and give some examples of it
is it local or long distance
Local
Paracrine signaling: signaling in which the target cell is close to the signal
releasing cell, and the signal chemical is broken down too quickly to be carried
to other parts of the body.
Example of Paracrine Signalling:
Insulin-like growth factor (IGF-1) signalling in
Melanoma
Clotting agents in thrombus formation
Inflammatory mediators e.g. TNFa
Describe neuronal/synaptic signalling and give an example
Is it local or long distance
Local
Synaptic signaling: from a nerve to a target cell (e.g. muscle)
Example: breathing: phrenic nerve (neutron) and diaphragm (muscle cells)
Describe autocrine signalling and give some examples
Is it local or long distance
Local
Autocrine signaling: is a form of signaling in which a cell secretes a chemical
messenger that signals the same cell.
Examples of Autocrine Signaling:
Cancer cells
Interleukin-I (IL-1) in monocytes (immune)
IL-2 signaling in T-cells
Give an example of endocrine cell signalling
insulin hormone: food eaten increased blood glucose release of insulin form pancreas insulin travels in the blood to stimulate glucose uptake into muscle liver and fat cells
What is the basic model of signal transduction pathways
extracellular signal molecule receptor protein intracellular signalling molecules effector proteins cell responses
Describe the mechanism of G-protein coupled receptor signalling and the role of G proteins
- GPCRs are proteins that span the membrane 7 times
- examples: adrenaline, acetylcholine, dopamine, light, olfaction
- active GPCRs trigger activation of G-proteins
- G-proteins are made up of alpha and betagama
subunits - inactive G-proteins contain GDP
bound to the a-subunit - activation of G-proteins by GPCR
swaps GDP for GTP - active G-protein can then activate
its effector and transmit the signal - signal turned off by the hydrolysis
of GTP –> GDP
G proteins operate as “switches” on cells
G-proteins activate enzymes that generate “second messengers” in the cell
Identify how Receptor Tyrosine kinase signalling functions, and the role
of tyrosine phosphorylation
- Enzyme coupled receptors
- Receptors form dimers that span plasma membrane once
- receptors arenezymes that phosphorylate tyrosine amino acids
- RTKs control cell growth, cell division and other ‘slower’ cellular responses
- on/off switch for RTKs depends on phosphorylation of tyrosine
Explain how G protein signalling is altered in infectious disease such as cholera
Target of cholera toxin is G protein called Gs
Cl- secretion into the gut is controlled by Gs protein and cAMP
Cholera toxin prevents GTP breakdown, keeping Gs in the “on” conformation, triggering excessive Cl- excretion
Cholera toxin modifies the Gs protein via ADP ribosylation (adding a big sugar group)
This keeps Gs protein switched “on” by preventing breakdown of GTP
This causes overproduction of cAMP and excess Cl- is pumped out of the gut epithelial cells
This causes water and other salts to be pumped out, causing dehydration, loss of electrolytes etc and diarrhoea
Describe how altered chloride ion channel signalling contributes to cystic fibrosis
Disease caused by a deletion in the gene for the cAMP-dependent chloride channel pump (CFTR) in airway epithelial cells
Epithelial cells cant pump Cl- out of the cells
This decreases water secretion from the cells
Causes increased viscosity of the mucus (thickening)
Patient more prone to bacterial infections because they don’t clear the mucus from their lungs
In one sentence describe how incorrect cell signalling causes cholera
Cholera toxin causes over-activation of G-proteins
In one sentence describe how incorrect cell signalling causes paralysis
Botulinum toxin - inhibition of synaptic signalling via blockage of ACh release
In one sentence describe how incorrect cell signalling causes cystic fibrosis
Mutations in Cl- ion channel - defective Cl- transport in lung
In one sentence describe how incorrect cell signalling causes Parkinson’s disease
Lack of dopamine signalling via its GPCR
In one sentence describe how incorrect cell signalling causes Muckle Well’s syndrome
Excessive IL-1 receptor signalling
In one sentence describe how incorrect cell signalling causes breast cancer
Over-activation of EGF receptor tyrosine kinase (RTK)
What is a nucleation site
Centrosome near the nucleus has y-tubulin rings and each ring serves as the starting point (nucleation site) for growth of a microtubule
The minus end of each tubule is embedded in the centrosome and growth occurs from the plus end
Describe dynamic instability of microtubules
Microtubules anchored in the centrosome can grow but also shrink independently of each other
Allows cells to undergo rapid remodelling
If the growing microtubule doesn’t attach to something it shrinks
If it attaches to something it forms a stable link with the centrosome
Allowing for a highly organised MT network and helps position organelles in a cell
How is microtubule dynamic instability regulated
Dynamic instability is regulated by G-proteins
Tubulin are G-proteins
Tubulin GTP forms the growing microtubule
When GTP is hydrolysed to GDP the tubule detaches and the microtubule shrinks
GTP = on GDP = off
How can the direction of microtubule growth create polarisation of a cell
Microtubules can be stabilised by binding to capping proteins at the plus ends of their filaments
Depending on the direction of growth this binding to capping proteins can lead to polarisation of a cell
What is the function of Lysyl hydroxylase and prolyl hydroxylase
Lysyl - adds OH to some lysines
Prolyl - adds OH to some prolines
How is collagen synthesised
It is produced as procollagen which has additional peptides on the end of the protein to prevent assembly into fibrils
Procollagen is secreted our of the cell
Cleavage of propeptides (done by procollagen proteinases)
Collagen fibres now in the extracellular matrix
What is the cause of Alport Syndrome
Mutations in genes for type IV collagen
Give an example of an enzyme that breaks down the cellular matrix
Matrix metalloproteinases
How do cells attach to the extracellular matrix
Adaptor molecule called fibronectin is needed
Cells bind fibronectin via transmembrane receptors called integrins
The integrins attach to the actin cytoskeleton and thus give the cel its tensile strength
What is the difference between a glycoprotein and a proteoglycan
Glycoprotein:
- proteins with covalently linked carbohydrate
Proteoglycan:
- extracellular proteins linked to complex negatively charged carbohydrates (GAGs)
- sugar is predominant
Name 4 functions of GAGs in the ECM
- space filling - resistance to compression
- regulation of molecular transport through the ECM
- bind and act as a reservoir for growth factors that signal to cells
- regulate cell migration and movement through the ECM
What is the basal lamina made up of
It is a specialised ECM
Mad up of type IV collagen and laminin
What is the function of tight junctions and what are they made up of
Leak proof seal between cells
Made up of proteins called claudins and occludins (ZO-1)
What is the function of adherens junction
Joins actin bundle in one cell to similar bundle in neighbouring cell
What is the function of desmosomes
Joins the intermediate filaments in one cell to those in a neighbour
What is the function of gap junctions
Forms channels that allow small water-soluble molecules, including ions, to pass from cell to cell
What is the function of hemidesmosomes
Anchors intermediate filaments in a cell to the basal lamina
What is entropy
The degree of randomness or disorder of a system - greater the disorder the greater the entropy
How is enzyme performance described through the Michaelis & Menten equation
The rate of a reaction (V) increases as the substrate increases, until a maximum is reached (Vmax) and is the point where all substrate binding sites are occupied
The Michaelis constant (Km) is the substrate concentration where half the maximum binding occurs (1/2Vmax)
The larger the Km, the weaker the substrate is bound to the enzyme
Give an example of a coupled reaction
Glucose ➡️ glucose-6-phosphate
Catalysed by hexokinase
What is ATP
Adenosine-5’-triphosphate
Energy
A molecule which contains three phosphates helped together by high energy bonds
When the third phosphate is cleaved, leaving ADP, energy is released to drive anabolic reactions
Briefly describe glycolysis
Does it require oxygen
Where does it occur
Glycolysis is the pathway where the energy from glucose is harvested to generate NADH and ATP
Anaerobic pathway - no oxygen required
Occurs in the cytoplasm
Draw the flow chart for glycolysis
See lecture 21
Slide 16
Draw the flow chart for the energy investment phase of glycolysis
Lecture 21
Slide 17
What is the enzyme involved in step 3 of the energy investment phase of glycolysis
Phosphofructokinase
Draw the flow chart for the cleavage phase of glycolysis
Lecture 21
Slide 19
Draw the flow chart for the energy generation phase of glycolysis
Lecture 21
Slide 21
What happens to the NADH of glycolysis
If oxygen is present the NADH is re-oxidised to NAD+ by the electron transport chain
However glycolysis is in the cytoplasm and the ETC is in the mitochondria - NADH cannot transverse the mitochondrial membrane
Therefore the hydrogens and electrons of each NADH are transferred to glycerol phosphate which can transport across the membrane
Here glycerate phosphate reacts with FAD to produce FADH2 and results in the formation of 2 ATPs per NADH
What happens to pyruvate when oxygen supply is limited. Draw the equation and name the enzyme involved
It is reduced to lactate (lactic acid)
Lecture 21
Slide 29
Enzyme = lactate dehydrogenase
What happens to pyruvate in conditions of adequate oxygen
It is transported from the cytoplasm to the mitochondria by a specific membrane transporter (pyruvate translocase)
It is then irreversible oxidatively decarboxylated to acetyl Co-enzymeA (CoA)
See lecture 21, slide 34 for equation
How many molecules of ATP does one molecule of NADH produce
3
How many molecules of ATP does one molecule of FADH2 produce
2
What are the products of one turn of the kreb cycle
3 NADH
1 GTP
1 FADH2
2 CO2
(One molecule of glucose produces 2 molecules of pyruvate/acetyl CoA - so therefore these values are really doubled if you are talking about how many per glucose molecule)
How many ATPs are generated per glucose molecule in total? How many from: glucose to pyruvate 2 pyruvate to 2 acetyl-CoA 2 x Kreb cycle
36
6
6
24
What happens in glycogenesis
Glucose is converted to glycogen
Glycogen is a glucose store
What happens in gluconeogenesis
6 high energy phosphate bonds are used to synthesise glucose from pyruvate
It is the only source of glucose during prolonged fasting
It occurs in the liver/kidneys
What is the difference between glucogenic and ketogenic amino acids
Glucogenic:
Are degraded to pyruvate or citric acid cycle intermediates
Can supply glucogenesis pathway
Ketogenic:
Degraded to acetyl CoA or acetoacetyl CoA
Can contribute to synthesis of fatty acids or ketone bodies
Which amino acids are ketogenic, glucogenic and both
Ketogenic:
Leucine
Lysine
Both: Isoleucine Phenylalanine Threonine Tryptophan Tyrosine
Glucogenic:
The rest
Which metabolic abnormality gives rise to the serious disease phenylketonuria?
A - homocysteine cannot be converted into methionine
B - phenylalanine cannot be converted into tyrosine
C - phenylalanine cannot be converted into alanine
D - tyrosine cannot be converted into phenylalanine
B
Where does the urea cycle occur
Mainly in the liver and to a lesser extent in the kindeys
What can be a result of urea cycle disorders
Very high circulating ammonium levels - life threatening
What is the cause of gout
Name some methods of treatment
Accumulation of uric acid or sodium urate in tissues
Caused by increased production or decreased excretion of uric acid
Alleviate joint pain and inflammation Avoid alcohol Avoid fructose rich drinks Increase renal excretion of uric acid - probenecid Inhibit xanthine oxidase - allopurinol
What is the cause and symptoms of Lesch-Nyhan Syndrome
Rare inherited X chromosome-linked recessive disorder
Complete loss of of HGPRT activity - reduces purine salvage - increases uric acid production
Describe how fatty acids are stored
Stored in the body as fat (triglyceride)
Predominantly in adipose tissue (in adipocytes)
How many ATPs are produced from one acetyl CoA
12
How many FADH2, NADH and acetyl CoAs are produced by shortening a fatty acid by 2 carbons
Shortening the fatty acid by 2 carbons yields:
1 FADH2
1 NADH
1 acetyl CoA
Describe lipolysis and B oxidation
Hormone sensitive adipose tissue lipase (HSL) released when body needs to mobilise energy stores
This regulates the release of fatty acids from stored triglycerides in adipose tissue
These can enter B-oxidation to provide energy (this occurs in the mitochondria)
Before oxidation the fatty acid is activated to fatty acyl-CoA in the outer mitochondria membrane - requires 1 ATP
B-oxidation is a 4 step cyclic process - takes off two carbons each cycle
Each cycle releases 1 acetyl-CoA, 1 FADH2 and 1 NADH
FADH2 and NADH enter electron transport chain
Acetyl-CoA can enter TCA cycle and produce more NADH and FADH2 (3 NADH, 1 GTP and 1 FADH)
Describe the condition of MCADD (medium chain acyl dehydrogenase deficiency)
Medium chain acyl CoA dehydrogenase deficiency is a fat oxidation disorder and is inherited in an autosomal recessive manner
Leads to a build up of medium-chain fats which can become toxic
Subjects must rely on glucose for energy
Life threatening
Describe briefly ketogenesis
If excess acetyl-CoA then it is converted to acetoacetyl CoA
This is then converted to ketone bodies (acetoacetate, B-hydroxybutyrate, acetone)
Occurs in the liver mitochondria
Important during fasting
What are ketone bodies
Water-soluble compounds that are produced as by-products when fatty acids are broken down for energy in the liver
Briefly describe lipogenesis
The process by which acetyl-CoA is converted to fatty acids, and subsequently triglycerides
Where does fatty acid synthesis take place
In the cytosol
What enzyme catalyses the first step (activation) of fatty acid synthesis
Acetyl-CoA carboxylase
Lipogenesis occurs in the cytoplasm and requires acetyl-CoA
But acetyl-CoA is generated in mitochondria and cannot cross the inner mitochondria membrane
How do we supply acetyl-CoA for lipogenesis?
Acetyl-CoA combines with oxaloacetate to produce citrate
Citrate is transported into cytoplasm via membrane transporter
Citrate then cleaved to form acetyl-CoA and oxaloacetate
Describe briefly the 3 steps of lipogensesis
- Activation:
- in cytoplasm
- acetyl-CoA carboxylate to malonyl-CoA
- catalysed by acetyl-CoA carboxylase - Elongation
- catalysed by fatty acid synthase complex
- adds two carbons at a time from malonyl-CoA with the loss of carbon dioxide
- repeats until 16 C are added - palmitic acid
- mainly occurs in the endoplasmic reticulum by enzymes called fatty acid elongates - Termination
- needs nerdy
- palmitic acid is a 16C saturated fatty acid - max length that can occur using this enzyme complex
-
How does HMG-CoA reductase maintain cholesterol homeostasis
High cholesterol:
- decrease HMG-CoA reductase transcription
- causes reduced cholesterol production
Low cholesterol:
- increased HMG-CoA reductase transcription
- increased cholesterol production
How do statins work
Inhibit HMG-CoA reductase - reduce cholesterol biosynthesis
Liver cells then begin to draw cholesterol out of circulation to make up for lack of synthesis
Thus circulating levels of cholesterol in the blood will fall
What is the enzyme involved in complex I of the electron transport chain and what does it do
NADH-coenzyme Q reductase
Transfers electrons from NADH to Coenzyme Q
What enzyme is involved in complex III of the ETC and what does it do
Coenzyme Q reductase
Transfers electrons from reduced CoQ to cytochrome c
What is the enzyme involved in complex IV of the ECT and what does it do
Cytochrome c oxidase
Transfers electrons from cytochrome c to O2
What is the enzyme involved in complex V of the ECT and what does it do
ATP synthase
Protons flow through this enzyme which uses energy to generate ATP
What enzyme is involved in complex II of the ECT and what does it do
Succinate-coenzyme Q reductase
Transfers electrons from FADH2 to CoQ
Where does oxidative phosphorylation occur
In the inner mitochondrial membrane
What is a reactive oxygen species (ROS)
Any free radical involving oxygen
What is meant by oxidative stress
General term used to describe the level of oxidative damage in a cell, tissue or organ caused by ROS
Reflects the balance between exposure to ROS and removal of them from the body
ROS can come from oxidative phosphorylation or also environmental ROS (eg smoke and pollutants)
How do cells limit the damage caused by reactive oxygen species
Contain two antioxidant systems:
1. Antioxidant enzymes
2. Antioxidant vitamins
They neutralise ROS, limiting damage
Name an enzyme involved in the enzymatic defence against oxidative stress
Superoxide dismutase
What might the symptoms be for acute presentation of an inherited metabolic disease
vomiting lethargy poor feeding siezures hypoglycaemia metabolic acidosis
What might be symptoms for chronic presentation of an inherited metabolic disease
failure to thrive organomegaly seizures developmental delay eye changes
Name 3 foods which are restricted in a diet for PKU?
Meat
Fish
Nuts
Dairy
What is the mode of inheritance for PKU?
Autosomal recessive
List 3 consequences of untreated PKU?
Fair skin and hair Intellectual impairment Epilepsy Movement disorder Autistic behaviour Eczema
What is the cause of PKU
genetic deficiency of Phenylalanine Hydroxylase
Phenylalanine and phenylpyruvate accumulate in blood and urine
What is the cause of medium chain acyl dehydrogenase deficiency (MCADD)
People with this condition cannot break down fatty acids properly, because they lack one of the enzymes needed (Acyl CoA dehydrogenase)
This leads to a build-up of medium chain fats which can become toxic. They also cannot break down fatty acids for energy so rely on glucose
Name 3 things involved in management of MCADD
- avoid prolonged fasting
- carbohydrates before bed
- breakfast on time
- advice regarding alcohol intake
- have an emergency plan in place
What causes urea cycle disorders/defects
Deficiency of one of the enzymes involved in the urea cycle
Urea cycle removes nitrogen from the blood and converts it to urea which can be excreted via urine
in urea cycle disorders the nitrogen accumulates in the form of ammonium which is a highly toxic substance and it cannot be removed from the body
What kind of inheritance is OTC (ornithine transcarbamoylase) deficiency
X linked recessive
How would you be able to diagnose a urea disorder (what are the signs)
- v high ammonia levels ***
- often mild alkalosis
- plasma amino acids - may be high glutamine, low arginine
- urine - orotic acid present
When should you suspect familial hypercholesterolaemia (FH)
when the total cholesterol is > 7.5 mmol/L
or
personal or familial history of premature coronary heart disease
Describe dysbetalipoproteinaemia - clinical features, diagnosis and treatment.
Clinical features:
- autosomal recessive inheritance
- needs a trigger, eg: obesity, diabetes, hypothyroidism or low oestrogen states in women
- Markedly raised cholesterol and triglycerides
- cutaneous lipid deposition
- premature cardiovascular disease
Treatment: - Lowering of LDL-cholesterol is the main aim - Occasionally lowering of triglycerides is necessary - Lifestyle changes can help: Diet Weight loss Exercise - Drugs are often required
How do statins work
- HMG CoA reductase inhibitors
- causes decrease cellular cholesterol conc
- this activates sterol regulatory element binding protein (SREBP) - up-regulates the gene encoding for LDL-receptor
- increased LDL-receptor expression increases uptake of plasma LDL thus decreasing plasma LDL concentration
How do fibrates work
- activate nuclear transcription factor PPARa
- modulation of target genes increases activity of lipoprotein lip and decrease synthesis of apo C-111
- this decreases VLDL and triglycerides
How does the drug Ezetimibe work
Neimann-pick C1 receptor inhibitor - inhibits gut cholesterol absorption
How do PCSK9-inhibitors work
Monoclonal antibodies against pro protein converts subtilising-like/kexin-9
fortnightly or monthly subcutaneous injection
Describe ketoacidosis
when large amounts of the ketone bodies acetoacetate and b-hydroxybutyrate are released from liver, the blood pH drops because they are acids
In the absence of glucose, ketone bodies can be used as an energy source, with the exception of the following?
a) Adipocytes
b) Brain
c) Erythrocytes
d) Muscle
e) Lungs
c - erythrocytes
The only source of glucose during prolonged fasting is:
Gluconeogenesis
Glycolysis
Glycogenolysis
Glycogenesis
Electron transport chain
gluconeogenesis
How does diabetes effect the hormone regulation of metabolism. How is it diagnosed and treated
- In diabetes, there is overproduction and underutilisation of glucose
- There is an overproduction of fatty acids from adipose tissue – the liver turns these into ketone bodies and lipoproteins (VLDL)
- Dentists occasionally may diagnose diabetes by the characteristic acetone smell on the breath (ketoacidosis)
- Complete absence of insulin (untreated Type 1 diabetes) can lead to diabetic ketoacidosis and coma
- Treatment is by insulin injection, fluid replacement and correcting blood pH
What is the kinetochore
Specialised complex of proteins where spindle MT attach to chromosomes
Name the three types of microtubules
astral microtubules
kinetochore microtubules
inter polar microtubules
What enzyme regulates the cell cycle
Cyclin dependent kinases (CDKs)
Briefly describe the cell cycle and its four phases
4 phases
G1:
Cells begin to gown
S:
Replicate
G2
Prepare for cell division
M
Cell division and cytokinesis
What is replicative senescence
When cells go into a state where they cannot divide ever again
What is the difference between necrosis and apoptosis
Apoptosis – programmed cell death – dies in coordinated way – no leakage
Necrosis – cell starts to die – part of this dying process its contents leak out – body reacts by initiating immune response – inflammation
What is the difference between extrinsic and intrinsic apoptosis
Extrinsic pathway:
- Activated by cell surface receptors
- Death receptors
- Activated by ligands binding to the receptors
Intrinsic pathway:
- Activated by events within cells
- Depends on mitochondria
- Release of cytochrome c which can work with other proteins to activate caspases
